Binding MOAD (Mother of All Databases)

TLDR: This work has searched the crystallography papers for all 5000+ structures and compiled binding data for 1375 of the protein–ligand complexes, which is the largest collection of binding data reported to date in the literature.

Abstract: Binding MOAD (Mother of All Data- bases) is the largest collection of high-quality, protein- ligand complexes available from the Protein Data Bank. At this time, Binding MOAD contains 5331 protein-ligand complexes comprised of 1780 unique protein families and 2630 unique ligands. We have searched the crystallography papers for all 5000 structures and compiled binding data for 1375 (26%) of the protein-ligand complexes. The binding-affinity data ranges 13 orders of magnitude. This is the largest collection of binding data reported to date in the literature. We have also addressed the issue of redun- dancy in the data. To create a nonredundant dataset, one protein from each of the 1780 protein families was chosen as a representative. Representatives were cho- sen by tightest binding, best resolution, etc. For the 1780 "best" complexes that comprise the nonredun- dant version of Binding MOAD, 475 (27%) have bind- ing data. This significant collection of protein-ligand complexes will be very useful in elucidating the bio- physical patterns of molecular recognition and enzy- matic regulation. The complexes with binding-affinity data will help in the development of improved scoring functions and structure-based drug discovery tech- niques. The dataset can be accessed at http://www. BindingMOAD.org. Proteins 2005;60:333-340.